Semiconductor manufacturing processes can take advantage of the high spatial resolution of transmission electron microscopy (TEM) for evaluation of critical dimensions (CDs), defects, process development, and process monitoring. TEM (or STEM) based evaluations generally require preparation of a thin specimen (typically referred to as a lamella). In some cases, ion beam milling is used to obtain a suitable portion of a larger specimen (referred to herein as a “chunk”) and the milled chunk is thinned as needed. Automated procedures have been developed for cutting and removing portions (chunks) of a substrate for evaluation. Thinning generally requires precise placement of the chunk so that a surface of interest is perpendicular to an ion beam that is used for thinning. If the sample is not suitably oriented, substrate features at different locations are milled differently. For example, in an SEM image 1400 shown in FIG. 14, substrate features 1402 are associated with appropriate substrate milling, while substrate features 1404 are partially milled through, and their actual shapes and sizes are not readily apparent. Angular alignment requires careful adjustment by an operator. Such alignment therefore is subject to operator error and can be slow, limiting the rate at which thinned lamella are produced. Improved alignment methods and apparatus are needed.